Cited by 866Genomics and Chromatin DynamicsDNA Repair MechanismsNuclear Structure and Function

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DNA loop extrusion by human cohesin

Davidson, Iain F., Bauer, Benedikt, Goetz, Daniela, Tang, Wen, Wutz, Gordana, Peters, Jan-Michael·2019·Science

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Abstract

Eukaryotic genomes are folded into loops and topologically associating domains, which contribute to chromatin structure, gene regulation, and gene recombination. These structures depend on cohesin, a ring-shaped DNA-entrapping adenosine triphosphatase (ATPase) complex that has been proposed to form loops by extrusion. Such an activity has been observed for condensin, which forms loops in mitosis, but not for cohesin. Using biochemical reconstitution, we found that single human cohesin complexes form DNA loops symmetrically at rates up to 2.1 kilo-base pairs per second. Loop formation and maintenance depend on cohesin's ATPase activity and on NIPBL-MAU2, but not on topological entrapment of DNA by cohesin. During loop formation, cohesin and NIPBL-MAU2 reside at the base of loops, which indicates that they generate loops by extrusion. Our results show that cohesin and NIPBL-MAU2 form an active holoenzyme that interacts with DNA either pseudo-topologically or non-topologically to extrude genomic interphase DNA into loops.

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Background
ATP dependent DNA transport within cohesin: Scc2 clamps DNA on top of engaged heads while Scc3 promotes entrapment within the SMC-kleisin ringPreprint
Collier, J., Lee, B., Roig, M. B., Yatskevich, S., Petela, N. J., Metson, J., Voulgaris, M., Llamazares, A. G., Löwe, J., & Nasmyth, K. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.06.03.132233 · Cited by 1
“That cohesin can associate with DNA in a functional manner without being topologically entrapped within S-K rings is supported by the finding that LE in vitro can be mediated by a version of human cohesin whose Smc1, Smc3, and kleisin subunits are expressed as a single polypeptide and whose hinge interface has been cr…”
BackgroundInfluential
Cohesin modulates DNA replication to preserve genome integrityPreprint
Wu, J., Liu, Y., Zhangding, Z., Liu, X., Chen, A., Gan, T., Liu, Y., Yin, J., Zhang, W., & Hu, J. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.06.471507 · Cited by 1
Rad21 is the core subunit of the cohesin complex involved in directing genome organizationPreprint
Sun, Y., Sun, Y., Xu, X., Zhao, W., Zhang, Y., Chen, K., Li, Y., Wang, X., Zhang, M., Xue, B., et al. (2021) · Research Square · doi:10.21203/rs.3.rs-1120640/v1 · Cited by 1
Transcriptional regulation and chromatin architecture maintenance are decoupled modular functions at the Sox2 locusPreprint
Taylor, T., Sikorska, N., Shchuka, V. M., Chahar, S., Ji, C., Macpherson, N. N., Moorthy, S. D., Mitchell, J. A., & Sexton, T. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.02.09.479674 · Cited by 1
“Long-range chromatin interactions are mediated by loop extrusion wherein the ring-like cohesin complex translocates bi-directionally along chromatin, bringing linearly distal regions near to one another (Davidson et al., 2019; Fudenberg et al., 2016; Li Y. et al., 2020; Sanborn et al., 2015).”
Background
The RAG1 N-terminal region regulates the efficiency and pathways of synapsis for V(D)J recombination
Beilinson, H., Glynn, R., Yadavalli, A., Xiao, J., Corbett, E., Saribasak, H., Arya, R., Miot, C., Bhattacharyya, A., Jones, J., et al. (2021) · immuneACCESS · doi:10.21417/hab2021jem · Cited by 1
Hi-TrAC reveals fine-scale chromatin structures organized by transcription factorsPreprint
Liu, S., Cao, Y., Cui, K., Tang, Q., & Zhao, K. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.01.494329 · Cited by 1
DNA capture and loop extrusion dynamics by cohesin-NIPBLPreprint
Kaur, P., Shi, Z.-B., Lu, X.-T., Zhang, H.-S., Finkelstein, I., Tao, Y., Yu, H.-T., & Wang, H. (2022) · bioRxiv · doi:10.1101/2022.08.18.504320 · Cited by 1
“Despite recent experimental demonstrations of DNA loop extrusion by cohesin and condensin in vitro and in cellulo (22,23,25,46,55-58), we have not reached a consensus regarding the molecular mechanism of DNA loop extrusion (36).”
BackgroundInfluential
Different NIPBL requirements of cohesin-STAG1 and cohesin-STAG2Preprint
Gil, D. A., Cuadrado, A., Giménez-Llorente, D., Rodríguez-Corsino, M., & Losada, A. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.11.29.518367 · Cited by 1
Nanofluidic Device for Manipulation and Modification of DNA by ProteinsPreprint
Dangi, S., Liu, M., Azad, Z., Countryman, P. J., Roushan, M., Livshits, G. I., Kaur, P., Pan, H., Shi, Z., Detwiler, A. C., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.12.29.521498 · Cited by 1
BRWD1 orchestrates chromatin topology by converting static to dynamic cohesin complexesPreprint
Mandal, M., Maienschein‐Cline, M., Hu, Y., Mohsin, A., Veselits, M., Wright, N. E., Okoreeh, M. K., Yoon, Y. M., Veselits, J., Georgopoulos, K., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.01.23.525212 · Cited by 1
What AlphaFold tells us about cohesin’s retention on and release from chromosomes
(2023) · doi:10.1101/2023.04.14.536858 · Cited by 1
What AlphaFold tells us about cohesin’s retention on and release from chromosomesPreprint
Nasmyth, K., Lee, B., Roig, M. B., & Löwe, J. (2023) · eLife · doi:10.7554/elife.88656.1 · Cited by 1
MethNet: a robust approach to identify regulatory hubs and their distal targets in cancerPreprint
Sakellaropoulos, T., Do, C., Jiang, G., Cova, G., Meyn, P., Dimartino, D., Ramaswami, S., Heguy, A., Tsirigos, A., & Skok, J. A. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.07.548142 · Cited by 1
RNA Pol II antagonises mitotic chromatin folding and chromosome segregation by condensinPreprint
Lebreton, J., Colin, L., Chatre, E., & Bernard, P. (2023) · bioRxiv · doi:10.1101/2023.08.08.552486 · Cited by 1
Biologic and clinical features of childhood gamma delta T-ALL: identification of STAG2/LMO2 γδ T-ALL as an extremely high risk leukemia in the very youngPreprint
Kimura, S., Pölönen, P., Montefiori, L. E., Park, C. S., Iacobucci, I., Yeoh, A. E. J., Attarbaschi, A., Moore, A. S., Brown, A., Manabe, A., et al. (2023) · medRxiv · doi:10.1101/2023.11.06.23298028 · Cited by 1
STAG2 mutations regulate 3D genome organization, chromatin loops, and Polycomb signaling in glioblastoma multiformePreprint
Waldman, T. A., Kim, J.-S., Xu, W., Yang, T., Ya, A., Tallon, L. J., Sadzewicz, L., Harris, B. T., Sarkaria, J. N., & Jin, F. (2023) · Research Square · doi:10.21203/rs.3.rs-3673198/v1 · Cited by 1
NSE5 subunit interacts with distant regions of the SMC arms in the Physcomitrium patens SMC5/6 complexPreprint
Vaculíková, J., Holá, M., Králová, B., Lelkes, E., Štefanovie, B., Vágnerová, R., Angelis, K. J., & Palecek, J. J. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.01.12.574989 · Cited by 1
Brain and cancer associated binding domain mutations provide insight into CTCF’s relationship with chromatin and its ability to act as a chromatin organizerPreprint
Skok, J. A., Do, C., Jiang, G., Cova, G., Katsifis, C. C., Narducci, D. N., Yang, J., Sakellaropoulos, T., Vidal, R. S., Lhoumaud, P., et al. (2024) · Research Square · doi:10.21203/rs.3.rs-4670379/v1 · Cited by 1
Context-dependent epigenome rewiring during neuronal differentiationPreprint
Manelli, V., Diwakar, J., Beşkardeş, S., Gil, D. A., Forné, I., Chong, F., Imhof, A., & Bonev, B. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.10.18.618996 · Cited by 1
“Consistent with this, we also observed that the levels of Mau2 (also known as Scc4), which together with Nipbl is required for cohesin loop extrusion 42 , were increased upon Neurog2 expression specifically in ES but not in NPC (Fig.”
Smc5/6 - microtubules binding shapes pericentromeric chromatinPreprint
Simon, À. C., Martuzzi, C., Isler, S., Batrin, R., Pinholt, H. D., Földes, T., Laflamme, G., Barbi, M., Mirny, L. A., D’Amours, D., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.13.623393 · Cited by 1
Replisomes restrict SMC-mediated DNA-loop extrusion in vivo
Liao, Q., Brandão, H. B., Ren, Z., & Wang, X. (2025) · doi:10.1101/2025.02.23.639750 · Cited by 1
SMC complex unidirectionally translocates DNA by coupling segment capture with an asymmetric kleisin pathPreprint
Yamauchi, M., Brandani, G. B., Terakawa, T., & Takada, S. (2025) · eLife · doi:10.7554/elife.106752.1 · Cited by 1
The mechanical code of DNA impacts its interaction with DNA gyrasePreprint
Forbes, B. G., Pinckney, R., Liu, S., Biswas, A., Potter, H., Morris, E. R., & Basu, A. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.10.21.683783 · Cited by 1
“…Host Factor (IHF) significantly bend DNA 33 , Structure Maintenance of Chromatin (SMC) proteins like cohesion extrude tight loops in the path of DNA 34 , nucleosomes 2 and their remodelling rely on extensive DNA bending and wrapping, viral packaging of DNA involves tight bending 3 , and DNA repair…”
AT-hook-dependent DNA loop extrusion by STAG1 drives 3D genome foldingPreprint
Sakata, R., Giménez-Llorente, D., Losada, A., & Nishiyama, T. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.17.688764 · Cited by 1
Classical enhancers couple cis -regulatory logic with transcriptional condensates and 3D genome architecturePreprint
Tiusanen, V., Patel, D., Xia, J., Xu, C., Datta, S., Yun, J. W., Cancellieri, S., Fei, L., Yilmaz, M., Pitkänen, E., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.23.701252 · Cited by 1
“…cohesin complex organizes interphase chromosomes into loops through active extrusion driven by structural maintenance of chromosomes (SMC) proteins 23-25, Convergently oriented CTCF sites act as barriers to extrusion 37,38 , creating topologically associating domains (TAD) 39-41 with frequent…”
Cryo-EM and single molecule visualization unravel the role of human condensin II activation by M18BP1 in driving DNA compactionPreprint
Borsellini, A., Chamera, S., Cecatiello, V., Andrecka, J., & Vannini, A. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.02.703226 · Cited by 1
“The activity of SMC complexes has been largely associated with the ability to form loops of DNA, as demonstrated by single molecule assays where individual complexes actively form loops of DNA in a process that is ATP dependent ( 8, 12, 34-36 ).”
Transcription directs Holliday junction branch migrationPreprint
Powell, T., Brown, G. G. B., Allison, R. M., Harper, J. A., Neale, M. J., & Gittens, W. H. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.13.711646 · Cited by 2

Authors: Davidson, I. F., Bauer, B., Goetz, D., Tang, W., Wutz, G., & Peters, J.-M.
Affiliations: Research Institute of Molecular Pathology (AT)
Corresponding author: Peters, Jan-Michael
ORCID: Davidson, Iain F.
Bauer, Benedikt
Wutz, Gordana
Peters, Jan-Michael
Venue: Science
Publisher: American Association for the Advancement of Science (AAAS)
Published: 2019-12-13
Volume: 366
Issue: 6471
Pages: 1338-1345
ISSN: 0036-8075 (ISSN-L)
1095-9203
DOI: 10.1126/science.aaz3418
OpenAlex: W2991248607
Cited by: 863
References: 46
Citations by year: 2026: 117 · 2025: 126 · 2024: 109 · 2023: 121 · 2022: 123 · 2021: 148 · 2020: 113 · 2019: 5
FWCI: 32.36
Type: journal article
Language: en
Open access: closed
Locations: Science (publishedVersion)
PubMed (publishedVersion)
Funders: Boehringer Ingelheim
European Molecular Biology Organization (Long-term Fellowship)
H2020 European Research Council (693949)
Human Frontier Science Program (Long-term Fellowship)
Austrian Research Promotion Agency (FFG-852936)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
Keywords: cohesin, DNA loop extrusion, topologically associating domains, chromatin folding, interphase chromatin, holoenzyme, condensin
MeSH terms: Cohesins, Chromosomal Proteins, Non-Histone, DNA, DNA-Binding Proteins, Proton-Translocating ATPases, HeLa Cells, Humans, Nucleic Acid Conformation, Cell Cycle Proteins, Holoenzymes

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DNA loop extrusion by human cohesin

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